Monday, December 31, 2012

Obviously, people blink in order to lubricate their eyes.
But that can’t be the only reason. We blink far more often than simple
moistening obligations would require. Plus, we seem to blink most at attention
break points—at the ends of written sentences or during pauses in speech. This
makes sense if you consider that each blink causes a momentary black-out of our
visual system. We’re blinking at times when we’ll miss the least amount of
information. Or are we looking at things the wrong way around? Researchers led
by Tamami Nakano of Osaka University showed that eyeblinks actually cause
attention disengagement rather than occurring after we’ve already briefly
disengaged.

In particular, the researchers were interested in two
regions of the brain: the dorsal attention network, which controls where we
focus our attention, and the default-mode network (DMN), which counteracts the
dorsal attention network and is involved in introspection. They placed ten
healthy volunteers in an fMRI while the subjects watched scenes from a TV show
(Mr. Bean). The subjects blinked an
average of 17.4 times per minute. They compared brain activity during the
spontaneous blinks to activity when the subjects were not blinking and to
moments when the screen was physically blacked out for the same duration and frequency
as normal eyeblinks.

The
scientists found that spontaneous eyeblinks activated the DMN and deactivated
the dorsal attention network. This was not true for screen blackouts, which
affected the visual areas of the brain, but not the attention allocating areas.
This suggests that we blink not because there’s been a break in our attention,
but in order to cause that break. Blinking may help us push forward to the next
image or line of dialogue.

Nakano T, Kato M, Morito Y, Itoi S, & Kitazawa S (2012). Blink-related momentary activation of the default mode network while viewing videos. Proceedings of the National Academy of Sciences of the United States of America PMID: 23267078.

Friday, December 28, 2012

Researchers from the Netherlands have been testing the
diagnostic powers of dogs. At least, they’ve been testing whether a two-year old beagle named Cliff can detect which
hospital patients are infected with Clostridium difficile. Not surprisingly, it turns out that he can.

C. difficile often
arises as a secondary infection in patients whose internal flora has been
decimated by antimicrobials. Unfortunately, it’s also extremely contagious,
requiring strict infection control. For this reason, the sooner patients with
this illness are identified the better. Patients with a C. difficile infection often have diarrhea with a distinctive
smell that even humans can detect well over half the time. The
researchers suspected that dogs could do much better than that. To that end,
they had professional detection dog instructor Hotsche Luik teach Cliff to
alert to the scent of C. difficile
in stool samples. This process took two months, and can be seen in the video at the bottom of the post.

For the testing phase, Cliff was presented with 100 stool
samples, half of which had come from C. difficile patients. The dog successfully identified all 50 C.
difficile samples. He gave an inconclusive
response to three of the negative samples.

Next, Cliff was walked through thirty ten-bed wards, each of which contained one C. difficile patient and nine controls without that illness. Cliff’s trainer,
who accompanied him, did not know which person out of the ten had C.
difficile. The dog correctly identified 25 out
of the 30 C. difficile patients
and 261 out of the 270 controls. In many of the cases in which Cliff gave an
inconclusive or incorrect response, he’d been distracted. For example, even
though the dog wasn’t supposed to interact with or touch the patients, some of
them offered him food or beckoned to him.

This
leads me to a large caveat about using detection dogs: their eagerness to
please their humans makes them susceptible to fudging the results (see my prior post about sniffer dogs). It’s not hard to envision that in a real hospital
setting, the nursing staff would have strong suspicions about which patients have
C. difficile, and this knowledge could very well influence the
dogs into providing the answers they think their humans want. That said, it
only took Cliff about ten minutes per ward. That’s a pretty quick and
completely noninvasive way to screen patients even if dogs do have a small
error rate.You can see Cliff in action below.

Thursday, December 27, 2012

Only a few animals have been shown to have ‘beat induction’,
that is the ability to perceive a regular beat or pulse. Interestingly, this
list has included birds, but not non-human primates. However, this deficit
could merely represent a lack of response to rhythms rather than an inability
to perceive those rhythms. In other words, just because an animal doesn’t bob
its head or tap its feet doesn’t mean that it hasn’t noticed the beat.

Researchers from the University of
Amsterdam and from the Universidad Nacional Autonoma de México decided to
bypass physical manifestations of beat induction and study actual brain
activity in two rhesus monkeys (Macaca mulatta). They played a drum pattern either in its entirety or
with specific notes omitted. Human adults and even newborn babies will notice
those missing elements. Was that true for the monkeys?

To find out, the researchers
looked for mismatch negativity in the monkeys’ brains. This occurs when
something unexpected occurs, such as when the incoming stimuli don’t match
expectations. For example, if you’re listening to a sound pattern and the music
skips a beat, this will activate mismatch negativity in your brain. It turns
out that while monkeys can detect rhythms based on the duration of sounds, they
can’t pick out the regularity, or beat, of those sounds the way humans and some
birds can.

The authors speculate that beat
induction emerged by convergent evolution in creatures that are able to mimic
sounds. If so, the ability to copy not only sounds but specific rhythms may
have been one of the factors involved in the acquisition of human language.

Wednesday, December 26, 2012

The U.S. Commerce Department's National Institute of Standards and Technology (NIST) has been experimenting with energy-efficient home design. They believe their model home 'Net Zero Energy Residential Test Facility', or NZERTF, will produce as much energy as it uses over the course of a year.Credit: NISTI would volunteer to test whether this house is as energy efficient as the researchers predict. How about you?

Monday, December 24, 2012

Despite the mothballing of the space shuttle program, public
and private funding for space travel is ongoing. Over the coming
decades, space tourism as well as jobs requiring work in space are expected to
climb. Both spaceports and new spacecrafts are in the planning or even construction
phases. However, there is one major deficiency. Apparently, there’s currently
no consensus on how to approve people for space travel. Researchers, led by
Marlene Grenon from the University of California, San Francisco, think we need
to remedy that lack.

Today, people who travel in space are almost uniformly fit
and healthy and most are in the first half of their lives. That won’t always be
the case. Grenon and her colleagues predict that doctors will one day be
fielding questions about whether heart patients can withstand liftoff forces or
about how long osteoporosis patients can safely live with low or no gravity.
Zero gravity can cause a host of problems even in healthy people, how will it
affect people who already have one or more infirmity?

So far, the evidence suggests that most people can tolerate
the forces (or lack of forces) associated with space travel, even if they have
pre-existing conditions. That said, we’re obviously far from knowing all there
is to know about the medical effects of space travel. At present, the FAA is
putting the onus of ensuring medical safety on the spacecraft operators, asking
only for informed consent. This in turn means that prospective travelers will
be seeking advice from their own doctors. For this reason, the researchers
suggest that physicians begin to compile data and resources to share with their
patients. The scientists have put together the following helpful chart as a
starting point.

Hypothetical
spaceflight considerations for common medical entities

Medical
condition

Influence
of spaceflight

Preflight
intervention

Coronary
artery disease

May
increase the risk for cardiac dysrhythmias or myocardial ischaemia

If
patient decides to fly, ensure that blood pressure and cardiac rhythm are
properly controlled

Cerebrovascular
disease

Possible
altered flow patterns in a carotid lesion

Optimise
medical treatment and consider repair as per current guidelines

Friday, December 21, 2012

In the 1880’s, Eadweard Muybridge (and no, that’s not his
original name. He was born Edward Muggeridge) pioneered photography of animals in motion. He’s most famous
for having solved the age-old riddle of whether all four of a horse’s hooves
ever leave the ground at once (answer: yes--see below).

Muybridge’s photographs put together into a film.

Since his experiments, we’ve had a better understanding of
animal locomotion, and this knowledge shows in post-Muybridge art work. The error rate for
correctly depicting animals in motion fell from 84% before his studies came to
light to 58% afterwards. Now, would you like to know how good prehistoric
people were at depicting moving animals? The error rate in cave art is 46%.

This interesting comparison is courtesy of some Hungarian
researchers led by Gabor Horvath of Eotvos University. They collected 1000
examples of art containing quadrupeds in motion. Their samples included both
2D (paintings, drawings, reliefs) and 3D (statues) art pieces. Because the
authors assume that there are 60 possible combinations for placement of all four feet (right forefoot in front and on the ground, right forefoot forward but raised in the air, etc.), 16 of which occur in nature, they come up
with an error rate for random foot placement of 73%. That is, before
Muybridge’s studies, people did worse than chance at depicting moving animals.

To see what the authors meant, let's look at a couple of examples. First, here's a drawing of a horse from
the Lascaux Caves in France.

Even if you're not sure where the ground would be in this drawing (is the left forefoot lifted?) this animal is anatomically
correct. Score one for cavemen. On the other hand, look at this pre-Muybridge modern drawing:

A
horse would only assume this posture with the left forefoot raised in front of the animal if the right hindfoot was behind the left hindfoot. Showing the animal with the right hind foot
placed forward is incorrect. Sorry Da Vinci.Horvath G, Farkas E, Boncz I, Blaho M, & Kriska G (2012). Cavemen were better at depicting quadruped walking than modern artists: erroneous walking illustrations in the fine arts from prehistory to today. PloS one, 7 (12) PMID: 23227149.

Thursday, December 20, 2012

The leading cause of food borne illness is not Escherichia coli or Salmonella. No,
that honor goes to the norovirus, a group of viruses named for the Norwalk
virus. Transmission of noroviruses can be via direct contact or contaminated
food or water. In general though, if you got sick with a norovirus, you
probably ate someone’s poo.

Most restaurants do their best to make sure their food is
safe. They use techniques known to kill bacteria such as E. coli. But how well do these food safety practices work
against a virus like the norovirus? To test this, researchers led by Lizanel
Feliciano from the Ohio State University allowed cream cheese contaminated with
either E. coli or norovirus stock
to harden onto ceramic plates and stainless steel forks. Contaminated milk was
left to dry in drinking glasses. The tableware was then washed with detergent
and sanitized with either chlorine-bleach or quaternary ammonium compounds.
Titers of bacteria or virus were taken both before and after air-drying and
washing.

Not surprisingly, the bacteria and viruses did fine on the
air-dried surfaces prior to cleaning. If a surface has been contaminated, the
bugs on it can survive for an extended period of time, up to a month in the
case of norovirus. Bacteria are more sensitive but can still last quite some
time.

Washing the tableware dropped the bacterial load
significantly. Unfortunately, that wasn’t the case for norovirus. There was a
reduction in the viral titer after washing, but not nearly enough to prevent
disease transmission. This was true for both mechanical and manual dishwashing
methods, though mechanical washing was slightly better at killing bacteria. Interestingly,
sanitization did not improve the outcomes for either bacteria or virus. The
greatest drop in microbe levels was achieved solely by washing, subsequent
sanitization was no better than spraying with tap water.

I should point out that it only takes a handful of norovirus
particles to cause an infection. In other words, you have to eliminate all
trace of the virus from tableware to ensure food safety. Standard washing
methods simply can’t achieve this goal, though vigilance on the part of restaurant management to ensure that sick people
stay out of the kitchen may do so. Bon appétit.

Wednesday, December 19, 2012

The Visual-ly Blog has a collection of 20 of the best infographics of 2012. They range from the beautiful to the fascinating. You can see the list here, but below are two of my favorites.Here are the color palettes for 10 artists over 10 years.

Tuesday, December 18, 2012

Does the memory of a large meal affect future hungriness?
According to researchers from the University of Bristol, led by Jeffrey
Brunstrom, yes, it can.

What I love most about this study is the self-filling soup
bowl used by the researchers. 100 participants were shown bowls containing
either 300 or 500 ml of soup. They proceeded to eat the soup. Unbeknownst to
the diners, the bowls had a secret filling/emptying system that covertly
changed the amount of soup in the bowls. Thus, the people who saw 300 ml in
their bowls were actually eating either 300 or 500 ml of soup. In the same way,
the people who were presented with 500 ml of soup actually ate either 300 or
500 ml. There were 25 people in each of these four groups.

You can see a diagram of the soup-filling apparatus below.
Volunteers were instructed to stop eating when the soup reached a certain line
in the bowl to ensure that they didn’t discover the filling apparatus at the
bottom (the total amount of soup was adjusted to account for this).

doi:10.1371/journal.pone.0050707.g001Only six people out of hundred noticed that the volume of soup
in their bowls was being manipulated. Those people were replaced with another
six volunteers.

The subjects had been asked to abstain from eating for at
least three hours before the test. After eating their soup, they were sent home
with a buzzer to remind them to rate their level of hunger every hour for the
next three hours. People who thought they had eaten 500 ml of soup but really
had only consumed 300 ml reported more satiety than people who consumed 500 ml
of soup but thought they had eaten 300 ml. In other words, the perception of
having eaten a large meal had a great effect than the actual amount ingested.

This
data suggests that if you wish to help a dieting friend, trick him into
thinking he’s consuming a larger portion than he really is. I can see a market
for a line of bowls with false bottoms that appear larger than they really are.

Monday, December 17, 2012

You know that not taking all your
antibiotics can lead to the evolution of drug resistant bacteria. You even know
that a much larger problem is the amount of antibiotics given to livestock. But
what you may not have realized is that the problem isn’t just that the bugs
living in animals will become drug resistant and then infect humans. No, a
bigger problem may be that bacteria living in soil can become resistant to
drugs pooped out of medicated animals. Yes, antibiotic resistance is being spread throughout our agricultural fields.

Researchers from Agriculture and
Agri-Food Canada applied a mix of sulfamethazine
(SMZ), tylosin (TYL), and chlortetracycline (CTC), three kinds of antibiotics common in livestock management, to fields annually for ten years. At the end of that
time, soil samples were taken and compared to similar fields that had not been
treated.

When the scientists added SMZ or
TYL to the samples, they found that the drugs biodegraded much more quickly
from fields that had previously been exposed to those drugs. In other words,
the bacteria in the virgin soils were far less equipped to deal with the influx
of antibiotics. In contrast, bacteria that had spent the last ten years in soil
containing antibiotics had adapted to those drugs. The scientists even
discovered at least one type of bacteria that was not only resistant but
appeared to actually use SMZ as a nutrient source.

This news isn’t necessarily bad. As long as the soil bacteria don’t
affect human health (and I realize that’s a big if), we might be able to employ
them to clean up fields before the drugs deposited there by livestock can leach
into water sources. Of course, we have little hope of cataloguing, let alone
managing, all the kinds of bacteria living in the dirt. So we’re all probably
better off if fewer drugs get deposited in those fields going forward.

Friday, December 14, 2012

When humans learn the names of
objects, they generally associate that name with the overall shape of the
object. Thus, if they are taught that a U-shaped object is called a ‘DAX’ and
asked to identify another DAX, they’ll pick an object with the same shape, but
not necessarily the same size or texture. In other words, when it comes to nomenclature, we generalize in a specific way with a bias toward shape. Is this true for dogs as well?

There are a handful of dogs with a
large enough vocabulary to test this feature of language. I’ve written before
about Chaser, who knows as many words as a human toddler (over a thousand).
This time, the test subject was a Border Collie named Gable, who reliably knows the names of over 40 different objects.Emile van der Zee, Helen Zulch and Daniel Mills from
the University of Lincoln and Gable's trainer taught the dog specific nonsense names for some novel objects. For example, in one
set of experiments, he was taught that the L-shaped object shown as (1) in the figure below
was a GNARK. When asked to retrieve another GNARK from amongst pairs of the
objects shown, he invariably chose something the same size (2 or 3) rather than
the same shape (4 or 7). Apparently, Gable was not making the same mental
associations that humans do.

I don’t know about you, but I’d say that if object 1 was presented to me as a GNARK, then
objects 4 and 7 are definitely GNARKS as well. This may be because, as a human,
I rely heavily on my eyesight to interpret the world. Dogs no doubt rely on
other cues, perhaps weight or mouth-feel. As you can see below, Gable does mouth each object before deciding which is the GNARK. Since word generalization is a critical feature in language, these data may mean that the way humans developed language is not the only road to that achievement.

Below, a test session in which Gable is asked to retrieve a u-shaped DAX. Between trials, the trainer lets Gable play with the DAX prototype. As the test begins, the researcher pretends to make that prototype one of the choices.

Test session in which Gable is asked to retrieve a u-shaped DAX. Between trials, the trainer lets Gable play with the DAX prototype. As the test begins, the researcher pretends to make that prototype one of the choices.Emile van der Zee, Helen Zulch, & Daniel Mills (2012). Word Generalization by a Dog (Canis familiaris): Is Shape Important? PloS ONE : doi:10.1371/journal.pone.0049382

Thursday, December 13, 2012

North American porcupine quills are notoriously easy to
stick into something but hard to pull back out. A dozen researchers from MIT,
Harvard, Xi’an Jiaotong University and Trinity College have now cracked the
puzzle as to why this is so. And in case you’re wondering why you should care,
consider that there are a lot of medical devices that also function by being
stuck into people.

Porcupine quills are composed of a black tip, typically a
few millimeters long, and a much longer white shaft. The tip contains
microscopic backward-facing barbs, each less than 50 microns (millionths of a
meter) across. The researchers compared normal porcupine quills to
quills that had been carefully sanded down to remove those tiny barbs without
altering the overall shape of the quill. The barbed quills required 54% less
penetration force than the sanded quills. Interestingly, it’s the region 2-4 mm
from the tip that’s critical for reducing penetration force, and not the very
tip. Quills with the barbs sanded down only in this region required
significantly more force to penetrate flesh regardless of whether the barbs in
the first 2 mm were intact.

It turns out that a barbed porcupine quill requires less penetration
force than an 18 gauge hypodermic needle. Though, to be fair, you’ll rarely
need to be stuck with such a large needle unless you’re giving blood. So, I
don’t think you’ll be seeing your doctor pull out a porcupine quill the next
time you get your flu shot. On the other hand, the backward facing barbs
somewhat counterintuitively result in a cleaner cut with less tissue damage.
This is despite the fact that the quills with barbs penetrate deeper into flesh
and are harder to remove. This characteristic may prove useful for implanting
medical devices.

And now, a random porcupine.

Woo Kyung Cho, James A. Ankrum, Dagang Guoa, Shawn A. Chester, & et al (2012). Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal Proceedings of the National Academy of Sciences of the United States of America : doi: 10.1073/pnas.1216441109.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.